chr19-55948044-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_176811.2(NLRP8):c.142G>A(p.Val48Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00766 in 1,614,080 control chromosomes in the GnomAD database, including 72 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_176811.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NLRP8 | NM_176811.2 | c.142G>A | p.Val48Met | missense_variant | 1/10 | ENST00000291971.7 | |
NLRP8 | NM_001317000.1 | c.142G>A | p.Val48Met | missense_variant | 1/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NLRP8 | ENST00000291971.7 | c.142G>A | p.Val48Met | missense_variant | 1/10 | 1 | NM_176811.2 | P2 | |
NLRP8 | ENST00000590542.1 | c.142G>A | p.Val48Met | missense_variant | 1/10 | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00752 AC: 1144AN: 152102Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00673 AC: 1690AN: 251292Hom.: 14 AF XY: 0.00687 AC XY: 933AN XY: 135846
GnomAD4 exome AF: 0.00767 AC: 11215AN: 1461860Hom.: 69 Cov.: 61 AF XY: 0.00745 AC XY: 5420AN XY: 727230
GnomAD4 genome ? AF: 0.00755 AC: 1150AN: 152220Hom.: 3 Cov.: 32 AF XY: 0.00786 AC XY: 585AN XY: 74416
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Oct 26, 2018 | This variant was classified as: Benign. The following ACMG criteria were applied in classifying this variant: BS1,BS2. - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2022 | NLRP8: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at